Problem in generating multiple metarigs
After you generate a rig, rename it. The armature generated is given the name rig, when you click generate on the second metarig the first rig is updated because of it's name.

This only applies up until 2.78, the about to be released blender 2.79 includes an updated rigify addon that makes this easier. The new version has options to overwrite or create a new rig, as well as choosing which rig to overwrite.